Gut Bacteria and Crohn’s Disease

Medically Reviewed by Minesh Khatri, MD on June 02, 2024
5 min read

Trillions of microbes live throughout your body. They include many species of bacteria, fungi, viruses, and even parasites. In your intestines, this population of microbes is called the gut microbiome.

When you’re healthy, these critters live in balance with each other. But when that balance is disrupted, it can make you more prone to disease, including Crohn’s disease.

Your gut microbes do all sorts of things, including:

  • Influence your immune system
  • Break down food compounds that could otherwise be toxic
  • Make vitamins and amino acids, including vitamins B and K
  • Prevent the overgrowth of harmful bacteria
  • Help you digest complex carbs like starch and fiber

When your body breaks down complex starches and fibers, it turns them into short-chain fatty acids (SCFAs). Scientists think SCFAs actually help prevent certain diseases, including some cancers as well as bowel disorders like Crohn’s.

The link between Crohn’s and the microbiome is complex, and researchers are still studying how it works. It involves many factors, including your genes, inflammation, and digestion.

We do know that people with Crohn’s and ulcerative colitis (the other main type of inflammatory bowel disease) have different microbiomes than those without it. Their gut microbiomes tend to have:

  • Less diverse communities of bacteria
  • Less of certain species that reduce inflammation

It’s not clear whether these changes might cause Crohn’s or whether they result from its symptoms or treatment. Certain things that raise your risk for Crohn’s, like “stomach flu” infections, smoking, and use of antibiotics early in life, also affect your microbiome.

The microbial imbalance in people with Crohn’s also could be related to things that happen during flares like:

  • Poor absorption of nutrients
  • Higher levels of water or blood in your intestines
  • More urgent bowel movements

Further, some people with Crohn’s have genetic changes (mutations) that affect the way their microbes interact with their immune systems. For example, certain genes might work in overdrive in their small intestines. This can cause too much inflammation there or make the environment less comfortable for “good” bacteria.

Some microbes in particular have emerged as culprits behind Crohn’s symptoms. During flare-ups, certain species, such as E. coli, take over. These can cause inflammation, and also out-compete other species that are good at producing SCFAs. This likely plays a role in the uncomfortable symptoms of Crohn’s.

People with Crohn’s also often have higher levels of a harmful bacteria called Klebsiella pneumoniae. This usually lives in the mouth. Although it’s an anaerobic bacteria (the type that grows without oxygen), it can thrive in places with some oxygen. When you have Crohn’s, the inflammation may cause higher oxygen levels in your gut. So Klebsiella can get a leg up over other microbes that can’t handle any oxygen. This can cause even more inflammation and worse symptoms.

Crohn's flare-ups can be a vicious cycle. The microbial imbalance could lead to worse symptoms, and in turn, those symptoms cause the gut to be even more unstable.

Diet can play a big role in the balance of bacteria in your gut. While each person’s microbiome is unique, and foods affect people in different ways, there are some general patterns.

Fiber is a key area to focus on. When you eat lots of fiber, this releases more SCFAs into your body. That makes the environment in your gut more acidic. This can hamper the growth of harmful bacteria such as Clostridium difficile and help maintain the growth of healthy “bugs.”

Foods with lots of fibers or starches that increase SCFAs include:

  • Garlic, onions, and leeks
  • Asparagus
  • Bananas
  • Seaweed
  • Fruits and vegetables
  • Beans
  • Whole grains such as wheat, oats, and barley

But some of these foods can also make you gassy and bloated. This can be especially uncomfortable for someone with Crohn’s, who may already struggle with these symptoms. Introduce them slowly, in small amounts at first, then gradually eat more over time. Your gastroenterologist and/or a dietitian can help you strike the right balance.

You can also eat foods that are natural probiotics, meaning they contain helpful live microbes. This includes fermented foods such as:

  • Kefir
  • Yogurt with active cultures
  • Pickled vegetables
  • Tempeh
  • Kombucha
  • Kimchi
  • Miso
  • Sauerkraut

Dietary fat also plays a role. A high-fat diet can affect your microbiome. Very high-fat diets may also trigger inflammation, not good for someone with Crohn’s.

However, the type of fat is important. Trans fats can cause issues even in small quantities. Omega-6 fatty acids, often found in processed foods, can make inflammation worse. Saturated fat can cause inflammation if you eat too much of it. Lots of saturated fat can also make your microbiome less diverse, leaving it vulnerable to takeover by harmful bacteria.

Understanding which fats are “good” and which are “bad” for Crohn’s can be confusing. For example, coconut oil has lots of saturated fat. But it may actually lower inflammation, so it may be good for you in small amounts.

Some research shows that, although monounsaturated fat is considered “good” fat, too much of it may reduce overall numbers of bacteria in your gut. This type of fat is found in olive oil, canola oil, avocados, and certain nuts and seeds.

So you may want to focus on anti-inflammatory foods with lots of polyunsaturated fats, like walnuts, sunflower seeds, tofu, and soybeans. A dietitian can help you understand what the research shows.

In general, although it’s OK to indulge now and then, avoid too much:

  • Corn, safflower, sunflower, soy, and vegetable oils, which may cause inflammation
  • Red meat, butter, and cheese, which are high in saturated fat
  • Artificial sweeteners, which may cause inflammation
  • Sugar, which can throw off your gut’s balance of bacteria
  • Fast and processed food

Avoid trans fats altogether. The FDA has banned the use of these fats, but you might still find low levels of them in fried or processed foods.

We don’t have enough research to know whether probiotic supplements might benefit people with Crohn’s.

For people who are healthy, with a well-balanced gut microbiome, probiotic supplements probably won’t do much.

But for people whose microbiomes are unstable or out of balance, probiotics may be helpful. This includes those who are very young or very old, or who have a condition or an event that disrupted the microbiome – for instance, if you had bad diarrhea after an illness, or took antibiotics that cleared out some of your healthy gut bacteria. Probiotics help restore balance by boosting your gut’s population of “good” bacteria such as Lactobacillus and Bifidobacterium.

But the FDA doesn’t regulate probiotic supplements, and labels can be misleading. If you have Crohn’s, talk to your doctor before taking any probiotics.